[R] Calculating RMSE in R from hurdle regression object

David March Morla
Wed, 12 Mar 2014 18:51:12 -0000

Dear Tim,

I think that in this paper you would find a suite of different metrics
to evaluate your hurdle model:
Potts, Joanne M., and Jane Elith. "Comparing species abundance
models."
Ecological Modelling 199.2 (2006): 153-163.

Best regards,
David March

El 12/03/2014 18:55, Tim Marcella escribi?:
> Hi,
>
> My data is characterized by many zeros (82%) and overdispersion. I have
> chosen to model with hurdle regression (pscl package) with a negative
> binomial distribution for the count data. In an effort to validate the
> model I would like to calculate the RMSE of the predicted vs. the observed
> values. From my reading I understand that this is the calculated on the raw
> residuals generated from the model output. This is the formula I used
>
> H1.RMSE <- sqrt(mean(H1$residuals^2))     # Where H1 is my fitted hurdle
> model
>
> I get 46.7 as the RMSE. This seems high to me based on the model results.
> Assuming my formula and my understanding of RMSE is correct (and please
> correct me if I am wrong) I question whether this is an appropriate use of
> validation for this particular structure of model. The hurdle model
> correctly predicts all of my zeros. The predictions I get from the fitted
> model are all values greater than zero. From my readings I understand that
> the predictions from the fitted hurdle model are means generated for the
> particular covariate environment based on the model coefficients. If this
> is truly the case it does not make sense to compare these means to the
> observations. This will generate large residuals (only 18% of the
> observations contain counts greater than 0, while the predicted counts all
> exceed 0). It seems like comparing apples to oranges. Other correlative
> tests (Pearson's r, Spearman's p) would seem to be comparing the
mean
> predicted value for particular covariate to the observed which again is
> heavily dominated by zeros.
>
> Any tips on how best to validate hurdle models in R?
>
> Thanks
>
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>
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David March Morl?
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